Seed dormancy—the temporary failure of a viable seed to germinate under favorable conditions—is a complex characteristic influenced by many genes and environmental factors. To detect the genetic factors associated with seed dormancy in rice, we conducted a QTL analysis using chromosome segment substitution lines (CSSLs) derived from a cross between Nona Bokra (strong dormancy) and Koshihikari (weak dormancy). Comparison of the levels of seed dormancy of the CSSLs and their recurrent parent Koshihikari revealed that two chromosomal regions—on the short arms of chromosomes 1 and 6—were involved in the variation in seed dormancy. Further genetic analyses using an F2 population derived from crosses between the CSSLs and Koshihikari confirmed the allelic differences and the chromosomal locations of three putative QTLs: Sdr6 on chromosome 1 and Sdr9 and Sdr10 on chromosome 6. The Nona Bokra alleles of the three QTLs were associated with decreased germination rate. We discuss the physiological features of the CSSLs and speculate on the possible mechanisms of dormancy in light of the newly detected QTLs.

The availability of a whole-genome sequenced mutant population and the cataloging of mutations of each line at a single-nucleotide resolution facilitate functional genomic analysis. To this end, we generated and sequenced a fast-neutron-induced mutant population in the model rice cultivar Kitaake (Oryza sativa L. ssp. japonica), which completes its life cycle in 9 weeks. We sequenced 1,504 mutant lines at 45-fold coverage and identified 91,513 mutations affecting 32,307 genes, i.e., 58% of all rice genes. We detected an average of 61 mutations per line. Mutation types include single base substitutions, deletions, insertions, inversions, translocations, and tandem duplications. We observed a high proportion of loss-of-function mutations. We identified an inversion affecting a single gene as the causative mutation for the short-grain phenotype in one mutant line. This result reveals the usefulness of the resource for efficient, cost-effective identification of genes conferring specific phenotypes. To facilitate public access to this genetic resource, we established an open access database called KitBase that provides access to sequence data and seed stocks. This population complements other available mutant collections and gene-editing technologies. This work demonstrates how inexpensive next-generation sequencing can be applied to generate a high-density catalog of mutations.

Rach Nui is a late Neolithic settlement of hunter-gatherers in southern Vietnam. However, the site also has a series of mortared floors corresponding to a sedentary lifestyle, where the inhabitants continued to live in the same area and repaired or replaced their floors over a period of 150 years. The inhabitants relied on a mixed economy that included domesticated and gathered plants, as well as hunted and managed animals. Although, there is evidence for the consumption of domesticated rice and foxtail millet, the inhabitants were mainly hunter-gatherers who relied on their surrounding mangrove and swamp forest habitats for most of their food requirements. From the archaeobotanical work done, it appears that the domesticated cereals, rice and foxtail millet, found at the site were imported. On the other hand, sedge nutlets and parenchyma were identified in high frequencies and were probably locally sourced, suggesting that foraging and/or vegeculture played a major role in the economy of Rach Nui

The prehistoric settlement of Madagascar by people from distant Southeast Asia has long captured both scholarly and public imagination, but on the ground evidence for this colonization has eluded archaeologists for decades. Our study provides the first, to our knowledge, archaeological evidence for an early Southeast Asian presence in Madagascar and reveals that this settlement extended to the Comoros. Our findings point to a complex Malagasy settlement history and open new research avenues for linguists, geneticists, and archaeologists to further study the timing and process of this population movement. They also provide insight into early processes of Indian Ocean biological exchange and in particular, Madagascar’s floral introductions, which account for one-tenth of its current vascular plant species diversity.

Dorian Q Fuller's insight:

This study documents that arrival of Asian rice in SE Africa and Madagascar from the 8th century AD

For the first time we integrate quantitative data on lithic sickles and archaeobotanical evidence for domestication and the evolution of plant economies from sites dated to the terminal Pleistocene and Early Holocene (ca. 12000–5000 cal. BCE) from throughout the Fertile Crescent region of Southwest Asia. We find a strong correlation in some regions, throughout the Levant, for increasing investment in sickles that tracks the evidence for increasing reliance on cereal crops, while evidence for morphological domestication in wheats (Triticum monococcum and Triticumdicoccum) and barley (Hordeum vulgare) was delayed in comparison to sickle use. These data indicate that while the co-increase of sickle blades and cereal crops support the protracted development of agricultural practice, sickles did not drive the initial stages of the domestication process but rather were a cultural adaptation to increasing reliance on cereals that were still undergoing selection for morphological change. For other regions, such as the Eastern Fertile Crescent and Cyprus such correlations are weaker or non-existent suggesting diverse cultural trajectories to cereal domestication. We conclude that sickles were an exaptation transferred to cereal harvesting and important in signalling a new cultural identity of “farmers”. Furthermore, the protracted process of technological and agricultural evolution calls into question hypotheses that the transition to agriculture was caused by any particular climatic event.

The prehistoric settlement of Madagascar by people from distant Southeast Asia has long captured both scholarly and public imagination, but on the ground evidence for this colonization has eluded archaeologists for decades. Our study provides the first, to our knowledge, archaeological evidence for an early Southeast Asian presence in Madagascar and reveals that this settlement extended to the Comoros. Our findings point to a complex Malagasy settlement history and open new research avenues for linguists, geneticists, and archaeologists to further study the timing and process of this population movement. They also provide insight into early processes of Indian Ocean biological exchange and in particular, Madagascar’s floral introductions, which account for one-tenth of its current vascular plant species diversity.

Rice (Oryza sativa) is regarded as the only grass that was selected for cultivation and eventual domestication in the Yangtze basin of China. Although both macro-fossils and micro-fossils of rice have been recovered from the Early Neolithic site of Shangshan, dating to more than 10,000 years before present (BP), we report evidence of phytolith and starch microfossils taken from stone tools, both for grinding and cutting, and cultural layers, that indicating barnyard grass (Echinochloa spp.) was

Dorian Q Fuller's insight:

Evidence for wild millet grass gathering and processing alongside rice in the millennia before clear evidence for the domestication process.

There are two models for the origins and timing of the Bronze Age in Southeast Asia. The first centres on the sites of Ban Chiang and Non Nok Tha in Northeast Thailand. It places the first evidence for bronze technology in about 2000 B.C., and identifies the origin by means of direct contact with specialists of the Seima Turbino metallurgical tradition of Central Eurasia. The second is based on the site of Ban Non Wat, 280 km southwest of Ban Chiang, where extensive radiocarbon dating places the transition into the Bronze Age in the 11th century B.C. with likely origins in a southward expansion of technological expertise rooted in the early states of the Yellow and Yangtze valleys, China. We have redated Ban Chiang and Non Nok Tha, as well as the sites of Ban Na Di and Ban Lum Khao, and here present 105 radiocarbon determinations that strongly support the latter model. The statistical analysis of the results using a Bayesian approach allows us to examine the data at a regional level, elucidate the timing of arrival of copper base technology in Southeast Asia and consider its social impact.

Dorian Q Fuller's insight:

The latest Bayesian chronology for the transition from the Neolithic to the Bronze Age in Thailand, based on quite alot of high quality dates. Among other things it highlights the discrepancy between a short chronology based on dates from burials bone and shell and an older long chronology based on dating the organic fraction of ceramics. While it has long been assumed that dating the organics from pottery dates that rice chaff temper, various studies make it apparent that there is old carbon (presumably from organic rich clays potters used) that confounds this. Here the pottery organics dates are around 700 years too old. This problem also affects other regions, like the middle Yangtze where ceramic "temper" dates from Pengtoushan are consistently almost a millennium too old compared to better dated contexts at Bashidang, or Saharan millet tempered ceramics that are around 500 years too old. While pottery impressions may be a useful way to mark the presence of a crop-- direct dates on pottery are not so reliable for fixing this presence in time.

The cultivation of rice has had a major impact on both societies and their environments in Asia, and in China in particular. Phytolith assemblages from three Neolithic sites in the Lower Yangtze valley reveal that in early rice fields the emphasis was on drainage to limit the amount of water and force the rice to produce seed. It was only in the later third millennium BC that the strategy changed and irrigated paddies came into use. The results demonstrate that plant remains, including weed assemblages, can reveal wetter or drier growing conditions, showing changes in rice cultivation from flooded and drained fields to large, intensively irrigated paddies.

Dorian Q Fuller's insight:

The phytolith wet:dry index applied to the evolution of rice in the Lower Yangtze

The existence of moated mounds in the archaeological record of north-east Thailand has long been known, the majority constructed during the earlier first millennium AD. Despite considerable research, the purpose of the substantial and sometimes multiple moats surrounding raised occupation mounds has remained a mystery. Combining locational, hydrological and rainfall data with the archaeological evidence, this study of the moated mounds of the Khorat Plateau seeks to resolve the question through statistical analysis. The results suggest that water storage may have been the primary purpose of the moats, enabling communities to survive dry seasons and droughts.

Dorian Q Fuller's insight:

Water storage that was likely important in irrigating rice and the Iron shift from rainfed to irrigated rice cultivation

Research by Dorian Fuller, UCL colleagues and collaborative partners is being featured in a special issue of the Proceedings of the National Academy of Sciences of the United States of America (PNAS). The papers are part of a collection entitled: "The Modern View of Domestication", edited by Greger Larson and Dolores R. Piperno, Special Feature of The Proceedings of the National Academy of Sciences, USA (29 April 2014). Early Edition online content is available now via the links below

Genetic improvements in plant breeding programs in local regions have led to the development of new cultivars with specific agronomic traits under environmental conditions and generated the unique genetic structures of local populations. Understanding historical changes in genome structures and phenotypic characteristics within local populations may be useful for identifying profitable genes and/or genetic resources and the creation of new gene combinations in plant breeding programs. In the present study, historical changes were elucidated in genome structures and phenotypic characteristics during 100-year rice breeding programs in Hokkaido, the northern limit of rice cultivation in the world. We selected 63 rice cultivars to represent the historical diversity of this local population from landraces to the current breeding lines. The results of the phylogenetic analysis demonstrated that these cultivars clearly differentiated into six groups over the history of rice breeding programs. Significant differences among these groups were detected in five of the seven traits, indicating that the differentiation of the Hokkaido rice population into these groups was correlated with these phenotypic changes. These results demonstrated that breeding practices in Hokkaido have created new genetic structures for adaptability to specific environmental conditions and breeding objectives. They also provide a new strategy for rice breeding programs in which such unique genes in local populations in the world can explore the genetic potentials of the local populations.

The origin of domesticated Asian rice (Oryza sativa) has been a contentious topic, with conflicting evidence for either single or multiple domestication of this key crop species. We examined the evolutionary history of domesticated rice by analyzing de novo assembled genomes from domesticated rice and its wild progenitors. Our results indicate multiple origins, where each domesticated rice subpopulation (japonica, indica, and aus) arose separately from progenitor O. rufipogon and/or O. nivara. Coalescence-based modeling of demographic parameters estimate that the first domesticated rice population to split off from O. rufipogon was O. sativa ssp. japonica, occurring at ∼13.1 – 24.1 kya, which is an order of magnitude older then the earliest archaeological date of domestication. This date is consistent, however, with the expansion of O. rufipogon populations after the Last Glacial Maximum ∼18 kya and archaeological evidence for early wild rice management in China. We also show that there is significant gene flow from japonica to both indica (∼17%) and aus (∼15%), which led to the transfer of domestication alleles from early-domesticated japonica to proto-indica and proto-aus populations. Our results provide support for a model in which different rice subspecies had separate origins, but that de novo domestication occurred only once, in O. sativa ssp. japonica, and introgressive hybridization from early japonica to proto-indica and proto-aus led to domesticated indica and aus rice.

Changing rice and millet arable systems were closely linked to social and environmental changes in Neolithic and Early Bronze Age in Central China. Two methods are used here to distinguish between rainfed millet farming and rice farming, using phytoliths from crop weeds found in ash middens and mixed cultural layer contexts. Samples were taken from three sites, Xipo and Huizui, in the Yellow River Valley in Henan, and Baligang which is situated towards the south of the province. The samples are from three cultural phases, Yangshao, Longshan and Erlitou. The phytoliths used are from grass leaves, so are not identified to genera or species but rather grouped into ecological categories, and canonical correspondence analysis was applied. Next, the ratios were calculated of phytolith morphotypes from cells that are genetically predisposed to form phytoliths (fixed), compared to silica bodies from cells that will form silica bodies when there is sufficient water uptake (sensitive). The results show differentiation between millet and rice and differences in how wet the rice fields were. The region experienced social and climate change throughout this time and this is reflected in the results

The period from the late third millennium BC to the start of the first millennium AD witnesses the first steps towards food globalization in which a significant number of important crops and animals, independently domesticated within China, India, Africa and West Asia, traversed Central Asia greatly increasing Eurasian agricultural diversity. This paper utilizes an archaeobotanical database (AsCAD), to explore evidence for these crop translocations along southern and northern routes of interaction between east and west. To begin, crop translocations from the Near East across India and Central Asia are examined for wheat (Triticum aestivum) and barley (Hordeum vulgare) from the eighth to the second millennia BC when they reach China. The case of pulses and flax (Linum usitatissimum) that only complete this journey in Han times (206 BC–AD 220), often never fully adopted, is also addressed. The discussion then turns to the Chinese millets, Panicum miliaceum and Setaria italica, peaches (Amygdalus persica) and apricots (Armeniaca vulgaris), tracing their movement from the fifth millennium to the second millennium BC when the Panicum miliaceum reaches Europe and Setaria italica Northern India, with peaches and apricots present in Kashmir and Swat. Finally, the translocation of japonica rice from China to India that gave rise to indica rice is considered, possibly dating to the second millennium BC. The routes these crops travelled include those to the north via the Inner Asia Mountain Corridor, across Middle Asia, where there is good evidence for wheat, barley and the Chinese millets. The case for japonica rice, apricots and peaches is less clear, and the northern route is contrasted with that through northeast India, Tibet and west China. Not all these journeys were synchronous, and this paper highlights the selective long-distance transport of crops as an alternative to demic-diffusion of farmers with a defined crop package.

Dorian Q Fuller's insight:

An updated treatment of the wider archaeological context of agricultural interchanges between East, West and South within which the hybrid origins of indica rice occurred.

The period from the late third millennium BC to the start of the first millennium AD witnesses the first steps towards food globalization in which a significant number of important crops and animals, independently domesticated within China, India, Africa and West Asia, traversed Central Asia greatly increasing Eurasian agricultural diversity. This paper utilizes an archaeobotanical database (AsCAD), to explore evidence for these crop translocations along southern and northern routes of interaction between east and west. To begin, crop translocations from the Near East across India and Central Asia are examined for wheat (Triticum aestivum) and barley (Hordeum vulgare) from the eighth to the second millennia BC when they reach China. The case of pulses and flax (Linum usitatissimum) that only complete this journey in Han times (206 BC–AD 220), often never fully adopted, is also addressed. The discussion then turns to the Chinese millets, Panicum miliaceum and Setaria italica, peaches (Amygdalus persica) and apricots (Armeniaca vulgaris), tracing their movement from the fifth millennium to the second millennium BC when the Panicum miliaceum reaches Europe and Setaria italica Northern India, with peaches and apricots present in Kashmir and Swat. Finally, the translocation of japonica rice from China to India that gave rise to indica rice is considered, possibly dating to the second millennium BC. The routes these crops travelled include those to the north via the Inner Asia Mountain Corridor, across Middle Asia, where there is good evidence for wheat, barley and the Chinese millets. The case for japonica rice, apricots and peaches is less clear, and the northern route is contrasted with that through northeast India, Tibet and west China. Not all these journeys were synchronous, and this paper highlights the selective long-distance transport of crops as an alternative to demic-diffusion of farmers with a defined crop package.

Rice (Oryza) is one of the world’s most important and productive staple foods, with highly diverse uses and varieties. We use archaeobotany, culture, history, and ethnobotany to trace the history of the development of sticky (or glutinous) forms. True sticky rice is the result of a genetic mutation that causes a loss of amylose starch but higher amylopectin content. These mutations are unknown in wild populations but have become important amongst cultivars in East and Southeast Asia (unlike other regions). In the same region, other cereals have also evolved parallel mutations that confer stickiness when cooked. This points to a strong role for cultural history and food preparation traditions in the genetic selection and breeding of Asian cereal varieties. The importance of sticky rice in ritual foods and alcoholic beverages in East and Southeast Asia also suggests the entanglement of crop varieties and culturally inherited food traditions and ritual symbolism.

Dorian Q Fuller's insight:

A review of the cultural importance of sticky rices throughout East and Southeast Asia with a model of their history that takes into account genetic evidence, archaeology, ancient history and the parallel evolution of other glutinous cereals like millets.

Agricultural origins and dispersals are subjects of fundamental importance to archaeology as well as many other scholarly disciplines. These investigations are world-wide in scope and require significant amounts of paleobotanical data attesting to the exploitation of wild progenitors of crop plants and subsequent domestication and spread. Accordingly, for the past few decades the development of methods for identifying the remains of wild and domesticated plant species has been a focus of paleo-ethnobotany. Phytolith analysis has increasingly taken its place as an important independent contributor of data in all areas of the globe, and the volume of literature on the subject is now both very substantial and disseminated in a range of international journals. In this paper, experts who have carried out the hands-on work review the utility and importance of phytolith analysis in documenting the domestication and dispersals of crop plants around the world. It will serve as an important resource both to paleo-ethnobotanists and other scholars interested in the development and spread of agriculture.

Dorian Q Fuller's insight:

Includes a summary of approaches to tracking rice in the archaeological phytolith record, including work from the UCL lab on rice cultivation ecology...

Baligang is a Neolithic site on a northern tributary of the middle Yangtze and provides a long archaeobotanical sequence from the Seventh Millennium BC upto the First Millennium BC. It provides evidence for developments in rice and millet agriculture influenced by shifting cultural affiliation with the north (Yangshao and Longshan) and south (Qujialing and Shijiahe) between 4300 and 1800 BC. This paper reports on plant macro-remains (seeds), from systematic flotation of 123 samples (1700 litres), producing more than 10,000 identifiable remains. The earliest Pre-Yangshao occupation of the sites provide evidence for cultivation of rice ( Oryza sativa ) between 6300–6700 BC. This rice appears already domesticated in on the basis of a dominance of non-shattering spikelet bases. However, in terms of grain size changes has not yet finished, as grains are still thinner than more recent domesaticated rice and are closer in grain shape to wild rices. This early rice was cultivated alongside collection of wild staple foods, especially acorns ( Quercus/Lithicarpus sensu lato). In later periods the sites has evidence for mixed farming of both rice and millets ( Setaria italica and Panicum miliaceum ). Soybean appears on the site in the Shijiahe period (ca.2500 BC) and wheat ( Triticum cf. aestivum ) in the Late Longshan levels (2200–1800 BC). Weed flora suggests an intensification of rice agriculture over time with increasing evidence of wetland weeds. We interpret these data as indicating early opportunistic cultivation of alluvial floodplains and some rainfed rice, developing into more systematic and probably irrigated cultivation starting in the Yangshao period, which intensified in the Qujialing and Shijiahe period, before a shift back to an emphasis on millets with the Late Longshan cultural influence from the north.

Dorian Q Fuller's insight:

An important archaeobotanical sequence from central China, which charts the rise and fall of millets versus rice in this regions between the Yangshao and the Shijiahe period. It also has a much earlier occupation (6300 BC) with non-shattering (domesticated) rice, which makes this earlier than evidence in the Lower Yangtze (or anywhere else at present), but presumably a separate domestication episode...

Important evidence for early domestication rice, which is highly non-shattering but still small-grained. This suggests these two trait may be evolving differentially in this region in contrast to the Lower Yangtze, but unfortunately we have no immediately earlier or later assemblages from the region to compare it with, so the extent to which this is a "dead end" or how it fits into a domestication trajectory remains to be determined.

Important evidence for early domestication rice, which is highly non-shattering but still small-grained. This suggests these two trait may be evolving differentially in this region in contrast to the Lower Yangtze, but unfortunately we have no immediately earlier or later assemblages from the region to compare it with, so the extent to which this is a "dead end" or how it fits into a domestication trajectory remains to be determined.

Once reserved for the exclusive use of Chinese royalty, black rice these days has become the darling of gourmets seeking superior nutrition. Now geneticists have traced where this rare rice came from.

Dorian Q Fuller's insight:

Black rice represents a post-domestication selection pathway from wild-type red to a deep dark purple, distinct from the better known selection to white (or light brown). Now we have some clear genetic indicators for the causation of this change-- even it it remains to challenge to determined when and where (and why) this took place.

We have compiled an extensive database of archaeological evidence for rice across Asia, including 400 sites from mainland East Asia, Southeast Asia and South Asia. This dataset is used to compare several models for the geographical origins of rice cultivation and infer the most likely region(s) for its origins and subsequent outward diffusion. The approach is based on regression modelling wherein goodness of fit is obtained from power law quantile regressions of the archaeologically inferred age versus a least-cost distance from the putative origin(s). The Fast Marching method is used to estimate the least-cost distances based on simple geographical features. The origin region that best fits the archaeobotanical data is also compared to other hypothetical geographical origins derived from the literature, including from genetics, archaeology and historical linguistics. The model that best fits all available archaeological evidence is a dual origin model with two centres for the cultivation and dispersal of rice focused on the Middle Yangtze and the Lower Yangtze valleys.

Dorian Q Fuller's insight:

The rice projects latest modelling effort: this is the first in a series of new models of rice's dispersal history, based on the RAD 2 (rice archaeological database), which can be explored in googleearth through the supplementary information.

29 April 2014. Cover of PNAS. The issue with the special feature on the "Modern View of Domestication". Cover image: Pictured are the Gamo-Gofa highlands of southern Ethiopia, a traditional agricultural landscape dotted with domesticated plants and animals such as hybrid cattle. Domesticated plants of diverse geographical origins include maize, sorghum, barley, Ethiopian banana, palm kale, and castor oil plant. The Modern View of Domestication Special Feature, appearing in this issue, presents recent genetic and archaeological evidence regarding the origin and spread of domesticated plants and animals, and addresses questions including those concerning the speed and intentionality of early domestication. See the Introduction to the Special Feature by Greger Larson et al. on pages 6139–6146. Image courtesy of Dorian Fuller.

Agriculture was a transformative development in the history of human societies and natural environments and drove the evolution of new domesticated species. Crop plants are the predominant domesticated species in most agricultural systems and are an essential component in all the food production systems that underpinned the development of urban societies. Archaeological plant remains provide a range of insights into the processes by which plants were domesticated in different parts of the world. The present paper provides a unique synthesis of evidence, including quantitative evidence on the trajectory and rate of domestication in seed crops and patterns in the development of tropical vegetatively propagated crops

Dorian Q Fuller's insight:

This paper includes the most upto date data on archaeologically documented domestication traits in rice, include non-shattering spikelet bases from China, and grain size change in both China and India.

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